Yes, but they do not seem to take passengers (although it could be worth enquiring).
They do take up to 12 passengers, though I suspect that any foot passenger availability would be very much on a stand-by basis.
One thing that hasn't been mentioned on here were the 1990-2004 era passenger ferries from Germany to Poland/Czech Republic which existed solely for selling industrial amounts of duty free goods. They were bordering on the ridiculous, often with highly absurd routes that made absolutely no sense if it wasn't for the huge profits made. The boats all had huge supermarkets inside, otherwise they only had very small passenger accommodation because, well, everyone was there to shop.
Altwarp (DE) - Nowe Warpno (PL). The border crossing still exists on the German side, although the infrastructure has been demolished on the Polish side. This route was ridiculously popular with both Polish and German customers, to the point where I believe they had up to four ships sailing to and from Poland at one time. It seems that in the early days, the ships didn't even bother calling at the 'other' harbour, they would just sail out of the port, into the other country, then turn back around to go back to the port. Poland and Germany then required ships to actually berth, so they would sail over, tie up very briefly, then go straight back, unless someone wanted to actually get off.
This route became less popular when Poland built a modern border crossing where they could actually check people inside, but it was very busy up until Poland joined the EU. Buses would run from both Szczecin and Berlin to here, for example.
Altwarp (DE) - Trzebież (PL). This one wasn't as popular, but Trzebież was preferred by Polish smugglers as the Polish Customs didn't have a modern facility to use there. It seems that at least one boat was diverted here from Nowe Warpno to take advantage of this, with the longer sailing time compensated for by the relatively loose customs controls.
Ahlbeck (DE) - Świnoujście (PL). I believe ferries also left from Heringsdorf to Świnoujście, though I'm not sure if it was the same ferry or if they ran separate ferries from both towns to Świnoujście. These were incredibly popular with German tourists in summer.
Gdynia (PL) - Baltiysk (RUS). This lasted up until very recently, and it was the last remaining duty free cruise in Polish waters. It was, by all accounts, quite a horrible route: you'd spend 4 hours each way at sea with the possibility of a bus trip around Kaliningrad for half an hour, and the sole purpose of this cruise was for people to drink a huge amount of duty free alcohol on board. Officially, it wasn't possible to drink what you'd bought on board, but in practice, no-one said a word. There was no possibility of staying in Kaliningrad, it was obligatory to return on the boat.
Gryfino (PL) - Gartz (DE). Another daft route, this one seemed to be quite popular with German tourists because of the lack of infrastructure in Gartz. It was the closest route to Berlin to my knowledge.
More to come...